Merge branch 'Jalview-JS/develop' into develop

[jalview.git] / src / jalview / gui / AppJmolBinding.java

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index eb15a65..75b98bc 100644 (file)
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -21,51 +21,40 @@
 package jalview.gui;
 
 import jalview.api.AlignmentViewPanel;
+import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.ext.jmol.JalviewJmolBinding;
+import jalview.io.DataSourceType;
 import jalview.structure.StructureSelectionManager;
+import jalview.util.Platform;
 
 import java.awt.Container;
+import java.io.File;
+import java.util.List;
 import java.util.Map;
 
 import org.jmol.api.JmolAppConsoleInterface;
-import org.jmol.java.BS;
-import org.openscience.jmol.app.jmolpanel.console.AppConsole;
+
+import javajs.util.BS;
 
 public class AppJmolBinding extends JalviewJmolBinding
 {
-  private AppJmol appJmolWindow;
-
-  private FeatureRenderer fr = null;
+  protected AppJmol appJmolWindow;
 
   public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
-          PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
-          String protocol)
+          PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
+          DataSourceType protocol)
   {
-    super(sSm, pdbentry, sequenceIs, chains, protocol);
+    super(sSm, pdbentry, sequenceIs, protocol);
     appJmolWindow = appJmol;
   }
 
   @Override
-  public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
+  protected IProgressIndicator getIProgressIndicator()
   {
-    AlignmentPanel ap = (alignment == null) ? appJmolWindow
-            .getAlignmentPanel() : (AlignmentPanel) alignment;
-    if (ap.av.isShowSequenceFeatures())
-    {
-      if (fr == null)
-      {
-        fr = (jalview.gui.FeatureRenderer) ap.cloneFeatureRenderer();
-      }
-      else
-      {
-        ap.updateFeatureRenderer(fr);
-      }
-    }
-
-    return fr;
+    return appJmolWindow.progressBar;
   }
 
   @Override
@@ -113,14 +102,18 @@ public class AppJmolBinding extends JalviewJmolBinding
     // appJmolWindow.repaint();
     javax.swing.SwingUtilities.invokeLater(new Runnable()
     {
+      @Override
       public void run()
       {
         appJmolWindow.updateTitleAndMenus();
+        // initiates a colourbySequence
+        // via seqColour_ActionPerformed.
         appJmolWindow.revalidate();
       }
     });
   }
 
+  @Override
   public void updateColours(Object source)
   {
     AlignmentPanel ap = (AlignmentPanel) source;
@@ -144,6 +137,7 @@ public class AppJmolBinding extends JalviewJmolBinding
     // msWalltime);
   }
 
+  @Override
   public void showUrl(String url)
   {
     showUrl(url, "jmol");
@@ -180,7 +174,7 @@ public class AppJmolBinding extends JalviewJmolBinding
           Container consolePanel, String buttonsToShow)
   {
     viewer.setJmolCallbackListener(this);
-    return new AppConsole(viewer, consolePanel, buttonsToShow);
+    return null;//BH can't do this yet. new AppConsole(viewer, consolePanel, buttonsToShow);
   }
 
   @Override
@@ -205,4 +199,38 @@ public class AppJmolBinding extends JalviewJmolBinding
     // TODO Auto-generated method stub
     return null;
   }
+
+  @Override
+  public JalviewStructureDisplayI getViewer()
+  {
+    return appJmolWindow;
+  }
+
+  @Override
+  public jalview.api.FeatureRenderer getFeatureRenderer(
+          AlignmentViewPanel alignment)
+  {
+    AlignmentPanel ap = (alignment == null)
+            ? appJmolWindow.getAlignmentPanel()
+            : (AlignmentPanel) alignment;
+    if (ap.av.isShowSequenceFeatures())
+    {
+      return ap.av.getAlignPanel().getSeqPanel().seqCanvas.fr;
+    }
+
+    return null;
+  }
+
+  @SuppressWarnings("unused")
+  public void cacheFiles(List<File> files)
+  {
+    if (files == null)
+    {
+      return;
+    }
+    for (File f : files)
+    {
+      Platform.cacheFileData(f);
+    }
+  }
 }